植物学报 ›› 2017, Vol. 52 ›› Issue (5): 590-597.DOI: 10.11983/CBB16137
收稿日期:
2016-06-21
接受日期:
2017-01-10
出版日期:
2017-09-01
发布日期:
2017-07-10
通讯作者:
包颖
基金资助:
Received:
2016-06-21
Accepted:
2017-01-10
Online:
2017-09-01
Published:
2017-07-10
Contact:
Ying Bao
摘要: 抗细胞凋亡基因(DAD)是一个高度保守的细胞凋亡抑制基因, 在植物生长发育中承担重要功能。为全面了解DAD基因在种子植物中的分布和演化规律, 该文利用31种植物的全基因组数据, 通过生物信息学手段, 深入探讨和分析了不同植物类群中DAD基因的拷贝数目、基因结构和染色体定位, 并综合另外7种裸子植物的转录组数据探讨了其在种子植物中的演化趋势。结果表明, DAD基因属于低拷贝基因, 在不同种子植物中只具有1-3个拷贝; 不同DAD基因编码的氨基酸长度在108-170 aa之间变动。同线性和系统发育分析进一步表明, 种子植物DAD基因的演化具有明显的谱系特异性。随机复制和染色体大片段复制及其随后的基因丢失可能是其维持低拷贝的重要方式。
包颖, 梅玉芹. 种子植物抗细胞凋亡DAD基因的演化. 植物学报, 2017, 52(5): 590-597.
Ying Bao, Yuqin Mei. Evolution of Defender Against Apoptotic Death (DAD) Genes in Seed Plants. Chinese Bulletin of Botany, 2017, 52(5): 590-597.
Taxa | Gene ID | Strand | Chromosome | Duplication pattern | Gene structure | Amino acid (aa) | |
---|---|---|---|---|---|---|---|
Intron | Exon | ||||||
Angiosperm | |||||||
Dicot | |||||||
Arabidopsis lyrata | AL1G33450 | _ | Scaffold_1 | Block | 4 | 5 | 115 |
AL4G20890 | + | Scaffold_4 | Block | 4 | 5 | 116 | |
A. thaliana | AT1G32210 | _ | Chr01 | Block | 4 | 5 | 115 |
AT2G35520 | + | Chr02 | Block | 4 | 5 | 116 | |
Brassica rapa | BR05G20160 | + | ChrA05 | Block | 4 | 5 | 115 |
BR09G26700a | + | ChrA09 | Block | 6 | 7 | 201 (88) d | |
Capsella rubella | CRU_001G29110 | _ | Scaffold_1 | Block | 4 | 5 | 115 |
CRU_004G16620 | + | Scaffold_4 | Block | 4 | 5 | 115 | |
Citrullus lanatus | CL10G00840 | + | Chr10 | 4 | 5 | 115 | |
Cucumis melo | CM00021G01290 | _ | Scaffold00021 | 4 | 5 | 115 | |
Eucalyptus grandis | EG0008G05930 | + | Scaffold_8 | 4 | 5 | 115 | |
Fragaria vesca | FV2G07670 | + | LG2 | 4 | 5 | 124 | |
Gossypium raimondii | GR03G18540 | + | Chr03 | Block | 4 | 5 | 117 |
GR08G22400 | _ | Chr08 | Block | 4 | 5 | 117 | |
Malus domestica | MD05G025840 | + | Chr05 | Random | 4 | 5 | 119 |
MD10G000120 | + | Chr10 | Random | 4 | 5 | 119 | |
Manihot esculenta | ME04430G00010 | + | Scaffold04430 | Random | 4 | 5 | 115 |
ME07304G00010 | + | Scaffold07304 | Random | 4 | 5 | 115 | |
Populus trichocarpa | PT01G13680 | _ | Chr01 | Block | 4 | 5 | 115 |
PT03G09680 | + | Chr03 | Block | 4 | 5 | 115 | |
Prunus persica | PPE_004G33460 | _ | Scaffold_4 | Block | 4 | 5 | 119 |
PPE_008G00790 | _ | Scaffold_8 | Block | 4 | 5 | 119 | |
Ricinus communis | RC29634G00390 | + | 29634 | Random | 4 | 5 | 115 |
RC30068G01440 | + | 30068 | Random | 4 | 5 | 113 | |
Solanum lycopersicum | SL08G076460 | + | Chr08 | 4 | 5 | 116 | |
S. tuberosum | ST08G008690 | _ | Chr08 | Block | 4 | 5 | 116 |
ST08G021840 | _ | Chr08 | Block | 4 | 5 | 116 | |
Thellungiella parvula | TP1G27890 | _ | Chr1-1 | 4 | 5 | 115 | |
Theobroma cacao | TC0003G30500 | + | Scaffold_3 | 4 | 5 | 116 | |
Vitis vinifera | VV02G01690 | + | Chr02 | 4 | 5 | 115 | |
Moncot | |||||||
Brachypodium distachyon | BD1G50180 | + | Chr01 | 4 | 5 | 114 | |
Hordeum vulgare | HV1571041G00020 | _ | Contig_1571041 | Random | 4 | 5 | 114 |
HV44460G00030 | + | Contig_44460 | Random | 4 | 5 | 114 | |
Oryza sativa | OS04G32550 | + | Chr04 | 4 | 5 | 114 | |
Setaria italica | SI004G00880 | + | Scaffold_4 | 4 | 5 | 114 | |
Sorghum bicolor | SB10G001000 | + | Chr10 | 4 | 5 | 114 | |
Zea mays | ZM09G06480 | _ | Chr09 | 4 | 5 | 114 | |
Musa acuminata | MA07G17850 | _ | Chr07 | Block | 4 | 5 | 115 |
MA10G06540b | _ | Chr10 | Block | - | 1 | 48 (22) d | |
MA11G08020 | + | Chr11 | Block | 4 | 5 | 170 | |
Basal taxon | |||||||
Amborella trichopoda | ATR_00025G00360 | + | Scaffold00025 | 4 | 5 | 121 | |
Gymnosperm | |||||||
Taxa | |||||||
Ginkgo bilobac Gnetum montanumc | Gene ID | Strand | Chromosome | Duplication pattern | Gene structure | Amino acid (aa) | |
Intron | Exon | ||||||
Picea abies | GBI00024938 | + | 6973 | - | - | 123 | |
GMO00028447 | _ | GTHK-0066600 | - | - | 113 | ||
PAB00021420a | _ | MA_128105 | Random | 5 | 6 | 162 (67) d | |
P. glaucac | PAB00041636 | _ | MA_42912 | Random | 4 | 5 | 115 |
PAB00057214b | + | MA_8328929 | Random | 1 | 2 | 50 (45) d | |
PGL00020840 | + | PUT-39823 PUT-39823 | - | - | 115 | ||
P. sitchensisc | PGL00013662 | + | PUT-23726 PUT-23726 | - | - | 115 | |
PGL00010558 | + | PUT-16509 | - | - | 115 | ||
Pinus pinasterc | PSI00016644 | + | PUT-531483 | - | - | 148 | |
PSI00008404 | + | PUT-21837 | - | - | 115 | ||
Pi. sylvestrisc | PPI00061658 | _ | Unigene30039 | - | - | 115 | |
PPI00006515 | _ | Cotig25413 | - | - | 115 | ||
PSY00006071 | _ | Isotig31028 | - | - | 115 | ||
Pi. taeda | PSY00026421 | + | Isotig68699 | - | - | 115 | |
PSY00004335 | + | isotig24244 | - | - | 115 | ||
PTA00003657 | _ | Scaffold464 | Random | 4 | 5 | 115 | |
Pseudotsuga menziesii c | PTA00022345b | + | Scaffold214279 | Random | 2 | 3 | 86 (72) d |
PTA00022344b | + | Scaffold214279 | Random | 1 | 2 | 44 (44) d | |
Moss Physcomitrella patens | PME00105748 | + | Psme_598296871 | - | - | 146 | |
PME00105747 | + | Psme_598296869 | - | - | 115 | ||
Alga Chlamydomonas reinhardtii | PP00045G01180 | + | Scaffold_45 | 4 | 5 | 131 | |
PP00456G00180 | - | Scaffold_456 | 4 | 5 | 114 |
表1 38种植物DAD同源基因的详细信息
Table 1 Detailed information of DAD homologous genes of 38 plants
Taxa | Gene ID | Strand | Chromosome | Duplication pattern | Gene structure | Amino acid (aa) | |
---|---|---|---|---|---|---|---|
Intron | Exon | ||||||
Angiosperm | |||||||
Dicot | |||||||
Arabidopsis lyrata | AL1G33450 | _ | Scaffold_1 | Block | 4 | 5 | 115 |
AL4G20890 | + | Scaffold_4 | Block | 4 | 5 | 116 | |
A. thaliana | AT1G32210 | _ | Chr01 | Block | 4 | 5 | 115 |
AT2G35520 | + | Chr02 | Block | 4 | 5 | 116 | |
Brassica rapa | BR05G20160 | + | ChrA05 | Block | 4 | 5 | 115 |
BR09G26700a | + | ChrA09 | Block | 6 | 7 | 201 (88) d | |
Capsella rubella | CRU_001G29110 | _ | Scaffold_1 | Block | 4 | 5 | 115 |
CRU_004G16620 | + | Scaffold_4 | Block | 4 | 5 | 115 | |
Citrullus lanatus | CL10G00840 | + | Chr10 | 4 | 5 | 115 | |
Cucumis melo | CM00021G01290 | _ | Scaffold00021 | 4 | 5 | 115 | |
Eucalyptus grandis | EG0008G05930 | + | Scaffold_8 | 4 | 5 | 115 | |
Fragaria vesca | FV2G07670 | + | LG2 | 4 | 5 | 124 | |
Gossypium raimondii | GR03G18540 | + | Chr03 | Block | 4 | 5 | 117 |
GR08G22400 | _ | Chr08 | Block | 4 | 5 | 117 | |
Malus domestica | MD05G025840 | + | Chr05 | Random | 4 | 5 | 119 |
MD10G000120 | + | Chr10 | Random | 4 | 5 | 119 | |
Manihot esculenta | ME04430G00010 | + | Scaffold04430 | Random | 4 | 5 | 115 |
ME07304G00010 | + | Scaffold07304 | Random | 4 | 5 | 115 | |
Populus trichocarpa | PT01G13680 | _ | Chr01 | Block | 4 | 5 | 115 |
PT03G09680 | + | Chr03 | Block | 4 | 5 | 115 | |
Prunus persica | PPE_004G33460 | _ | Scaffold_4 | Block | 4 | 5 | 119 |
PPE_008G00790 | _ | Scaffold_8 | Block | 4 | 5 | 119 | |
Ricinus communis | RC29634G00390 | + | 29634 | Random | 4 | 5 | 115 |
RC30068G01440 | + | 30068 | Random | 4 | 5 | 113 | |
Solanum lycopersicum | SL08G076460 | + | Chr08 | 4 | 5 | 116 | |
S. tuberosum | ST08G008690 | _ | Chr08 | Block | 4 | 5 | 116 |
ST08G021840 | _ | Chr08 | Block | 4 | 5 | 116 | |
Thellungiella parvula | TP1G27890 | _ | Chr1-1 | 4 | 5 | 115 | |
Theobroma cacao | TC0003G30500 | + | Scaffold_3 | 4 | 5 | 116 | |
Vitis vinifera | VV02G01690 | + | Chr02 | 4 | 5 | 115 | |
Moncot | |||||||
Brachypodium distachyon | BD1G50180 | + | Chr01 | 4 | 5 | 114 | |
Hordeum vulgare | HV1571041G00020 | _ | Contig_1571041 | Random | 4 | 5 | 114 |
HV44460G00030 | + | Contig_44460 | Random | 4 | 5 | 114 | |
Oryza sativa | OS04G32550 | + | Chr04 | 4 | 5 | 114 | |
Setaria italica | SI004G00880 | + | Scaffold_4 | 4 | 5 | 114 | |
Sorghum bicolor | SB10G001000 | + | Chr10 | 4 | 5 | 114 | |
Zea mays | ZM09G06480 | _ | Chr09 | 4 | 5 | 114 | |
Musa acuminata | MA07G17850 | _ | Chr07 | Block | 4 | 5 | 115 |
MA10G06540b | _ | Chr10 | Block | - | 1 | 48 (22) d | |
MA11G08020 | + | Chr11 | Block | 4 | 5 | 170 | |
Basal taxon | |||||||
Amborella trichopoda | ATR_00025G00360 | + | Scaffold00025 | 4 | 5 | 121 | |
Gymnosperm | |||||||
Taxa | |||||||
Ginkgo bilobac Gnetum montanumc | Gene ID | Strand | Chromosome | Duplication pattern | Gene structure | Amino acid (aa) | |
Intron | Exon | ||||||
Picea abies | GBI00024938 | + | 6973 | - | - | 123 | |
GMO00028447 | _ | GTHK-0066600 | - | - | 113 | ||
PAB00021420a | _ | MA_128105 | Random | 5 | 6 | 162 (67) d | |
P. glaucac | PAB00041636 | _ | MA_42912 | Random | 4 | 5 | 115 |
PAB00057214b | + | MA_8328929 | Random | 1 | 2 | 50 (45) d | |
PGL00020840 | + | PUT-39823 PUT-39823 | - | - | 115 | ||
P. sitchensisc | PGL00013662 | + | PUT-23726 PUT-23726 | - | - | 115 | |
PGL00010558 | + | PUT-16509 | - | - | 115 | ||
Pinus pinasterc | PSI00016644 | + | PUT-531483 | - | - | 148 | |
PSI00008404 | + | PUT-21837 | - | - | 115 | ||
Pi. sylvestrisc | PPI00061658 | _ | Unigene30039 | - | - | 115 | |
PPI00006515 | _ | Cotig25413 | - | - | 115 | ||
PSY00006071 | _ | Isotig31028 | - | - | 115 | ||
Pi. taeda | PSY00026421 | + | Isotig68699 | - | - | 115 | |
PSY00004335 | + | isotig24244 | - | - | 115 | ||
PTA00003657 | _ | Scaffold464 | Random | 4 | 5 | 115 | |
Pseudotsuga menziesii c | PTA00022345b | + | Scaffold214279 | Random | 2 | 3 | 86 (72) d |
PTA00022344b | + | Scaffold214279 | Random | 1 | 2 | 44 (44) d | |
Moss Physcomitrella patens | PME00105748 | + | Psme_598296871 | - | - | 146 | |
PME00105747 | + | Psme_598296869 | - | - | 115 | ||
Alga Chlamydomonas reinhardtii | PP00045G01180 | + | Scaffold_45 | 4 | 5 | 131 | |
PP00456G00180 | - | Scaffold_456 | 4 | 5 | 114 |
图1 基于38种植物的58条DAD基因的编码序列构建的最大似然性系统发育关系树分支附近的数值分别代表最大似然性分析中大于50%的自展支持率和贝叶斯分析中的后验率, 各基因位点同表1。
Figure 1 Maximum likelihood tree of DAD genes based on 58 amino acid sequences of 38 plantsNumbers near branches represent bootstrap values (>50%) of the maximum likelihood analysis and posterior rate of the Bayesian analysis. The gene loci in this figure are the same as those listed in Table 1.
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